It can add it, but it cannot catch it, because AkelPad itself sinks(exactly it transforms it, but never mind) it before any plugin can receive it.
Use ResHacker to change accelerators VK_F6 in accelerator resource of AkelPad 1031 to any other, which you do not plan to assign in HotKeys plugin, for instance VK_F7, VK_F8.
Or just use another other than F6 and Shift+F6 hotkey.